You pretty much answered your own question. You would need a battery isolator. Hellroaring's isolators are pretty popular in the offroad world, though they can be a bit pricy. The featureset on them, particularly the manual override/"self jumpstart" is awesome.

The positives from each battery would go to lugs on the isolator, and so would the alternator. When 12v key-on voltage is put into a terminal on the isolator, it bridges the batteries together so they can charge. When that voltage it pulled off, it separates the alternator, and each battery.